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Pipeline publication

[…] Table S4. Experiments were performed 3-times and unpaired t-test were used to calculate the p values., Libraries were prepared using TruSeq ChIP Library Preparation kit following the manufacturer’s instructions (Illumina). Libraries are checked for concentration and quality on DNA chips with a Bioanalyser (Agilent). The libraries were quantified by fluorimetric measurements with the Qubit® dsDNA HS Assay Kit (ThermoFisher). 65-bp and 130-bp Single Read sequences were generated on the Hiseq2500 sequencer according to manufacturer’s instructions (Illumina). Library statistics are provided in Supplemental Table S5., Illumina reads were aligned to the S. pombe genome assembly ASM294v2.23 using Bowtie v2.1.0 with default parameters and multi-mapper reads randomly distributed. Using BamTools , read counts were normalized to reads per million per kilo base (RPKM), using the total library size and a bin size of 1 kb. For the analysis of multi-mapper reads, we filtered aligned read files with samtools using the parameter -q 10., ChIP peaks versus appropriate inputs (whole-cell extracts) were called using MACS v2.1.0 . Statistic validation of peaks was performed using the IDR method with ENCODE recommendations . Genome browser tracks and meta-analysis were created using enrichment (IP reads per million (RPM) / input RPM) of indicated sequencing. Intersection of lists of peaks were calculated with BEDTools v.2.17.02 (parameters: -u). For the transcriptional analysis 2 groups of 108 genes were defined and intersected with the list of peaks shared by Lsd1/2 and Sap1. The first group contains the 108 most present transcripts and the 108 less present transcripts using the normalized data from ., We used a script to extract the beginning of reads that map on the Watson or Crick strands. Enrichments of 5' count were obtained using the total library size. p-values were obtained using the negative binomial distribution fitting function in R., All scripts used for the analysis and outputs are available upon request., All supplemental data for this article are also available online at http://m […]

Pipeline specifications

Software tools Bowtie, BamTools, SAMtools, BEDTools